That is very very peculiar!
as far as I know REFMAC doesnt really care whether you call something
ATOM or HETATM .
I suspect the problem is either in the cif file describing the co-factor
- could the atom type fpr MO be set as N? or possibly in the PDB file -
is the Atom name displaced to the left, and is the atom type (last
columns) set to MO?
Eleanor
James Pauff wrote:
Good morning/day/evening all,
I have a structure that is refined, with the exception
of the molybdenum (MoOOS) cofactors (there are two of
them), which are square pyramidal and coordinated to 2
sulfurs in an enedithiolate of a pterin ring. I have
brought up my issues with refining this before in
REFMAC, but something just dawned on me as I work
through/with it.
Although I define the Mo, O1, O2, S atoms as ATOM
records in the PDB, with restrained refinement in
REFMAC, the resulting *_refmac1.pdb file converts the
MO to a N. If I define the 4 atoms above as HETATM
records, the same happens with the output PDB,
changing all 4 atoms back to ATOM records and
redefining the MO as N.
I am also still getting problems with the connectivity
of the atoms in the coordination sphere of the
molybdenum, but that may be a side issue to this
confusing problem with the record lines in my output
PDBs here.
Thank you,
Jim
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